The color command colors atoms, atom labels, molecular surfaces, and vdw surfaces. Nonmolecular graphical objects are unaffected. Using ~color sets the color to none (no color assigned).
Color_name can be a built-in name or a name defined previously with colordef. In addition, special color names are:
| element | color |
|---|---|
| C | gray |
| N | blue |
| O | red |
| S | yellow |
| H,D,0-9 | white |
| F,CL,BR,I | magenta |
| B,FE | gray |
| others | cyan |
The optional specifiers b, l, s, and v designate atoms/bonds, atom labels, molecular surfaces, and vdw surfaces, respectively. When b is used to indicate "bonds," in actuality the specified atoms are colored and the bonds merely reflect the color(s) of the atoms. The specifier l allows atom labels to be colored differently than the associated atoms. (Note that the colors of bond labels and pseudobond labels are not affected. One way to color such a label is to select the bond or pseudobond and use the Selection Inspector to change its label color.) In the absence of a specifier, atoms, labels, and surfaces are all affected. The specifiers do not need to be comma-separated when used with ~color.
The atom-spec indicates which atoms (and/or associated labels or surfaces) are to be colored. If no atom-spec is given, all atoms (and/or their associated labels or surfaces) are affected.
In Chimera, visible color is determined by a hierarchy: per-atom colors overrule color settings at the model level. The color command always sets colors at the atom level. Modelcolor sets colors at the model level. Surfcolor sets which level is used as the source for visible surface colors; this must be the atom level for color to control the visible surface color.
Examples:
color green #2:his- color all histidine residues in model 2 green, as well as any associated labels, molecular surface, and van der Waals surface
color magenta,s #3- color the molecular surface of model 3 magenta
~color bl #0:4- remove the color assignments of atoms in the fourth residue of model 0 and their labels (the color will default to the model-level color)
color red @/color=blue- color red every atom that is blue (and any labels and surfaces associated with those atoms)
See also: colordef, bondcolor, ribcolor, modelcolor, surfcolor, rainbow, rangecolor, tcolor, the Actions menu